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!Series_title "Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative [cohort 3273]" |
!Series_geo_accession "GSE96058" |
!Series_status "Public on Mar 12 2018" |
!Series_submission_date "Mar 09 2017" |
!Series_last_update_date "May 04 2022" |
!Series_pubmed_id "32913985" |
!Series_pubmed_id "32926574" |
!Series_pubmed_id "33937624" |
!Series_pubmed_id "35304506" |
!Series_summary "PURPOSE" |
!Series_summary "In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers... |
!Series_summary "" |
!Series_summary "METHODS" |
!Series_summary "In total, 3,678 patients with BC were studied. For 405 tumors, a comprehensive multi-rater histopathologic evaluation was performed. Using RNA-seq data, single-gene classifiers and multigene classifiers (MGCs) were trained on consensus histopathology labels. Trained classifiers were tested on a prospec... |
!Series_summary "" |
!Series_summary "RESULTS" |
!Series_summary "Pathologist concordance was high for ER, PgR, and HER2 (average κ, 0.920, 0.891, and 0.899, respectively) but moderate for Ki67 and NHG (average κ, 0.734 and 0.581). Concordance between RNA-seq classifiers and histopathology for the independent cohort of 3,273 was similar to interpathologist concordanc... |
!Series_summary "" |
!Series_summary "CONCLUSION" |
!Series_summary "Classification error rates for RNA-seq–based classifiers for the five key BC biomarkers generally were equivalent to conventional histopathology. However, RNA-seq classifiers provided added clinical value in particular for tumors determined by histopathology to be hormone responsive but by RNA-seq to b... |
!Series_overall_design "Illumina paired-end RNA-sequencing and expression estimation were performed for two cohorts: a training cohort with 405 samples (GSE81538), and a validation cohort with 3273 samples (of which 136 cases have technical replicates) (GSE96058). A comprehensive histopathological evaluation was perfo... |
!Series_overall_design "" |
!Series_overall_design "Please note that there are ""primary sample"" (e.g F30) and ""technical replicate"" (e.g. F30repl) of the same BioSample. The technical replicates in herein are primarily newly constructed and sequenced libraries from the same RNA extraction as the primary sample, with the remaining replicates ... |
!Series_overall_design "" |
!Series_overall_design "Due to the patient consent, Swedish law, the potential that the sequencing data contains personally-identifiable information and hereditary mutations, and the right to privacy, the submitter cannot make available the raw sequence data in a public repository." |
!Series_type "Expression profiling by high throughput sequencing" |
!Series_contributor "Christian,,Brueffer" |
!Series_contributor "Johan,,Vallon-Christersson" |
!Series_contributor "Dorthe,,Grabau" |
!Series_contributor "Anna,,Ehinger" |
!Series_contributor "Jari,,Häkkinen" |
!Series_contributor "Cecilia,,Hegardt" |
!Series_contributor "Janne,,Malina" |
!Series_contributor "Yilun,,Chen" |
!Series_contributor "Pär-Ola,,Bendahl" |
!Series_contributor "Jonas,,Manjer" |
!Series_contributor "Martin,,Malmberg" |
!Series_contributor "Christer,,Larsson" |
!Series_contributor "Niklas,,Loman" |
!Series_contributor "Lisa,,Rydén" |
!Series_contributor "Åke,,Borg" |
!Series_contributor "Lao,H,Saal" |
!Series_sample_id "GSM2528079 GSM2528080 GSM2528081 GSM2528082 GSM2528083 GSM2528084 GSM2528085 GSM2528086 GSM2528087 GSM2528088 GSM2528089 GSM2528090 GSM2528091 GSM2528092 GSM2528093 GSM2528094 GSM2528095 GSM2528096 GSM2528097 GSM2528098 GSM2528099 GSM2528100 GSM2528101 GSM2528102 GSM2528103 GSM2528104 GSM2528105 GSM2... |
!Series_contact_name "Lao,H,Saal" |
!Series_contact_email "lao.saal@med.lu.se" |
!Series_contact_laboratory "Translational Oncogenomics Unit" |
!Series_contact_department "Department of Oncology and Pathology" |
!Series_contact_institute "Lund University" |
!Series_contact_address "Scheelevägen 2, MV404B2" |
!Series_contact_city "Lund" |
!Series_contact_zip/postal_code "22391" |
!Series_contact_country "Sweden" |
!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96058/suppl/GSE96058_UCSC_hg38_knownGenes_22sep2014.gtf.gz" |
!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96058/suppl/GSE96058_gene_expression_3273_samples_and_136_replicates_transformed.csv.gz" |
!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96058/suppl/GSE96058_transcript_expression_3273_samples_and_136_replicates.csv.gz" |
!Series_citation "Christian Brueffer, Johan Vallon-Christersson, Dorthe Grabau, Anna Ehinger, Jari Häkkinen, Cecilia Hegardt, Janne Malina, Yilun Chen, Pär-Ola Bendahl, Jonas Manjer, Martin Malmberg, Christer Larsson, Niklas Loman, Lisa Rydén, Åke Borg, and Lao H. Saal. Clinical Value of RNA Sequencing-Based Classifier... |
!Series_platform_id "GPL11154" |
!Series_platform_id "GPL18573" |
!Series_platform_taxid "9606" |
!Series_sample_taxid "9606" |
!Series_relation "SubSeries of: GSE81540" |
!Series_relation "BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA378692" |
!Sample_title "F1" "F2" "F3" "F4" "F5" "F6" "F9" "F10" "F11" "F12" "F13" "F14" "F15" "F16" "F17" "F18" "F19" "F20" "F21" "F22" "F23" "F24" "F25" "F26" "F27" "F28" "F29" "F30" "F31" "F32" "F33" "F34" "F35" "F36" "F37" "F38" "F39" "F40" "F41" "F42" "F43" "F44" "F45" "F46" "F47" "F48" "F49" "F50" "F51" "F52" "F53" "F54" "... |
!Sample_geo_accession "GSM2528079" "GSM2528080" "GSM2528081" "GSM2528082" "GSM2528083" "GSM2528084" "GSM2528087" "GSM2528088" "GSM2528089" "GSM2528090" "GSM2528091" "GSM2528092" "GSM2528093" "GSM2528094" "GSM2528095" "GSM2528096" "GSM2528097" "GSM2528098" "GSM2528099" "GSM2528100" "GSM2528101" "GSM2528102" "GSM2528103"... |
!Sample_status "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12... |
!Sample_submission_date "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "M... |
!Sample_last_update_date "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "... |
!Sample_type "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "... |
!Sample_channel_count "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1... |
!Sample_source_name_ch1 "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumo... |
!Sample_organism_ch1 "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"... |
!Sample_characteristics_ch1 "scan-b external id: Q008818.C008840.S000215.l.r.m2.c.lib.g.k.a.t" "scan-b external id: Q008769.C008792.S000250.l.r.m.c.lib.g.k.a.t" "scan-b external id: Q008568.C008577.S000424.l.r.m3.c.lib.g.k.a.t" "scan-b external id: Q008909.C009000.S000084.l.r.m.c.lib.g.k.a.t" "scan-b external id: Q0087... |
!Sample_characteristics_ch1 "instrument model: HiSeq 2000" "instrument model: HiSeq 2000" "instrument model: HiSeq 2000" "instrument model: HiSeq 2000" "instrument model: HiSeq 2000" "instrument model: HiSeq 2000" "instrument model: HiSeq 2000" "instrument model: HiSeq 2000" "instrument model: HiSeq 2000" "instrument m... |
!Sample_characteristics_ch1 "age at diagnosis: 43" "age at diagnosis: 48" "age at diagnosis: 69" "age at diagnosis: 39" "age at diagnosis: 73" "age at diagnosis: 40" "age at diagnosis: 82" "age at diagnosis: 67" "age at diagnosis: 71" "age at diagnosis: 64" "age at diagnosis: 78" "age at diagnosis: 44" "age at diagnosi... |
!Sample_characteristics_ch1 "tumor size: 9" "tumor size: 14" "tumor size: 27" "tumor size: 51" "tumor size: 60" "tumor size: 13" "tumor size: 10" "tumor size: 6" "tumor size: 16" "tumor size: 17" "tumor size: 32" "tumor size: 15" "tumor size: 17" "tumor size: 12" "tumor size: 15" "tumor size: 11" "tumor size: 14" "tumo... |
!Sample_characteristics_ch1 "lymph node group: NodeNegative" "lymph node group: 1to3" "lymph node group: 4toX" "lymph node group: 1to3" "lymph node group: 4toX" "lymph node group: NodeNegative" "lymph node group: NodeNegative" "lymph node group: NodeNegative" "lymph node group: 1to3" "lymph node group: 1to3" "lymph nod... |
!Sample_characteristics_ch1 "lymph node status: NodeNegative" "lymph node status: NodePositive" "lymph node status: NodePositive" "lymph node status: NodePositive" "lymph node status: NodePositive" "lymph node status: NodeNegative" "lymph node status: NodeNegative" "lymph node status: NodeNegative" "lymph node status: ... |
!Sample_characteristics_ch1 "er status: NA" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: NA" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: NA" "er status: NA" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er... |
!Sample_characteristics_ch1 "pgr status: NA" "pgr status: 1" "pgr status: 1" "pgr status: NA" "pgr status: NA" "pgr status: NA" "pgr status: NA" "pgr status: NA" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status: NA" "pgr status: NA" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status:... |
!Sample_characteristics_ch1 "her2 status: 0" "her2 status: 0" "her2 status: 0" "her2 status: 1" "her2 status: 0" "her2 status: 0" "her2 status: 1" "her2 status: 1" "her2 status: 0" "her2 status: 1" "her2 status: 0" "her2 status: 0" "her2 status: 0" "her2 status: 0" "her2 status: 0" "her2 status: 0" "her2 status: 0" "he... |
!Sample_characteristics_ch1 "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki6... |
!Sample_characteristics_ch1 "nhg: G3" "nhg: G2" "nhg: G3" "nhg: G3" "nhg: G2" "nhg: G3" "nhg: G1" "nhg: G3" "nhg: G2" "nhg: G3" "nhg: G2" "nhg: G2" "nhg: G3" "nhg: G3" "nhg: G1" "nhg: G1" "nhg: G1" "nhg: G1" "nhg: G3" "nhg: G2" "nhg: G2" "nhg: G1" "nhg: G2" "nhg: G2" "nhg: G3" "nhg: G3" "nhg: G3" "nhg: G3" "nhg: G1" "n... |
!Sample_characteristics_ch1 "er prediction mgc: 0" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 0" "er prediction mgc: 0" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction m... |
!Sample_characteristics_ch1 "pgr prediction mgc: 0" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 0" "pgr prediction mgc: 0" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr... |
!Sample_characteristics_ch1 "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 1" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 1" "her2 prediction mgc: 1" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction ... |
!Sample_characteristics_ch1 "ki67 prediction mgc: 1" "ki67 prediction mgc: 0" "ki67 prediction mgc: 1" "ki67 prediction mgc: 1" "ki67 prediction mgc: 0" "ki67 prediction mgc: 1" "ki67 prediction mgc: 0" "ki67 prediction mgc: 0" "ki67 prediction mgc: 0" "ki67 prediction mgc: 1" "ki67 prediction mgc: 0" "ki67 prediction ... |
!Sample_characteristics_ch1 "nhg prediction mgc: G3" "nhg prediction mgc: G2" "nhg prediction mgc: G3" "nhg prediction mgc: G3" "nhg prediction mgc: G2" "nhg prediction mgc: G3" "nhg prediction mgc: G2" "nhg prediction mgc: G2" "nhg prediction mgc: G2" "nhg prediction mgc: G3" "nhg prediction mgc: G2" "nhg prediction m... |
!Sample_characteristics_ch1 "er prediction sgc: 0" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 0" "er prediction sgc: 0" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction s... |
!Sample_characteristics_ch1 "pgr prediction sgc: 0" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 0" "pgr prediction sgc: 0" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr... |
!Sample_characteristics_ch1 "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 1" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 1" "her2 prediction sgc: 1" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction ... |
!Sample_characteristics_ch1 "ki67 prediction sgc: 1" "ki67 prediction sgc: 0" "ki67 prediction sgc: 1" "ki67 prediction sgc: 1" "ki67 prediction sgc: 0" "ki67 prediction sgc: 1" "ki67 prediction sgc: 0" "ki67 prediction sgc: 0" "ki67 prediction sgc: 0" "ki67 prediction sgc: 1" "ki67 prediction sgc: 0" "ki67 prediction ... |
!Sample_characteristics_ch1 "pam50 subtype: Basal" "pam50 subtype: LumA" "pam50 subtype: LumB" "pam50 subtype: LumA" "pam50 subtype: Normal" "pam50 subtype: Basal" "pam50 subtype: Her2" "pam50 subtype: LumA" "pam50 subtype: LumA" "pam50 subtype: LumB" "pam50 subtype: LumA" "pam50 subtype: LumA" "pam50 subtype: LumA" "p... |
!Sample_characteristics_ch1 "overall survival days: 2367" "overall survival days: 2367" "overall survival days: 2168" "overall survival days: 2416" "overall survival days: 2389" "overall survival days: 2373" "overall survival days: 2380" "overall survival days: 2324" "overall survival days: 2367" "overall survival days... |
!Sample_characteristics_ch1 "overall survival event: 0" "overall survival event: 0" "overall survival event: 1" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 1" "overall sur... |
!Sample_characteristics_ch1 "endocrine treated: 0" "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 0" "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 0" "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 1" "endocrine treat... |
!Sample_characteristics_ch1 "chemo treated: 1" "chemo treated: 1" "chemo treated: 1" "chemo treated: 1" "chemo treated: 0" "chemo treated: 1" "chemo treated: 0" "chemo treated: 1" "chemo treated: 0" "chemo treated: 1" "chemo treated: 0" "chemo treated: 0" "chemo treated: 1" "chemo treated: 1" "chemo treated: 1" "chemo ... |
!Sample_molecule_ch1 "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA"... |
!Sample_extract_protocol_ch1 "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "Q... |
!Sample_extract_protocol_ch1 "Poly(A) mRNA is isolated from the total RNA in up to 96-well microtiter plate format by two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen) using a KingFisher Flex magnetic particle processor (ThermoScientific). Zinc-mediated fragmentation (Ambion) is performed and the frag... |
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